AP Supplier with Multiple Bank Payments

We have suppliers that are set up with multiple banks(remit-tos). When we create invoices we change the bank to the correct one where the check should be sent. If we pay two invoices for the same supplier(same check run) and had chosen different banks on invoice entry, upon payment they are lumped together and sent to just one of the banks. Short of creating a separate supplier record for every supplier/bank combination what have others done to get around this issue?